WO2013006443A2 - Découverte d'une mutation somatique dans le gène myd88 du lymphome lymphoblasmocytaire - Google Patents

Découverte d'une mutation somatique dans le gène myd88 du lymphome lymphoblasmocytaire Download PDF

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WO2013006443A2
WO2013006443A2 PCT/US2012/044956 US2012044956W WO2013006443A2 WO 2013006443 A2 WO2013006443 A2 WO 2013006443A2 US 2012044956 W US2012044956 W US 2012044956W WO 2013006443 A2 WO2013006443 A2 WO 2013006443A2
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mutation
myd88
chromosome
biological sample
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PCT/US2012/044956
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WO2013006443A3 (fr
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Steven P. TREON
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Dana-Farber Cancer Institute, Inc.
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Priority to EP12807230.3A priority Critical patent/EP2726634B1/fr
Priority to US14/128,241 priority patent/US10465247B2/en
Priority to ES12807230.3T priority patent/ES2624981T3/es
Priority to CA2840687A priority patent/CA2840687C/fr
Publication of WO2013006443A2 publication Critical patent/WO2013006443A2/fr
Publication of WO2013006443A3 publication Critical patent/WO2013006443A3/fr
Priority to US16/580,523 priority patent/US11739385B2/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • WM Waldenstrom's macroglobulinemia
  • LPL lymphoplasmacytic lymphoma
  • Genetic factors play an important role in the pathogenesis of WM, with 25% of patients demonstrating a family history.
  • IgM monoclonal gammopathy of unknown significance (MGUS) often precedes the development of WM.
  • the primary oncogenetic event resulting in malignant transformation in WM remains to be delineated. Knowledge of such genomic alteration(s) may permit advances in diagnostic testing, and development of targeted therapies.
  • the invention involves,
  • lymphoplasmacytic lymphoma facilitating the diagnosis of lymphoplasmacytic lymphoma in a subject by selecting a subject on the basis that the subject presents one or more of the following clinical features: anemia, hyper-viscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, adenopathy, and an IgM serum paraprotein, obtaining a biological sample of the subject, and determining from the biological sample whether the subject has a mutation at position 38182641 in chromosome 3p22.2, wherein the presence of the mutation is indicative that the subject has lymphoplasmacytic lymphoma.
  • the subject presents two or more of the clinical features.
  • the subject presents three or more of the clinical features.
  • said determining comprises performing an assay to interrogate position 38182641 in chromosome 3p22.2.
  • the assay comprises allele specific polymerase chain reaction performed using. an allele specific primer, wherein the allele specific primer hybridizes at or near its 3' end to the mutation at position
  • the allele specific primer is SEQ ID NO: 5.
  • a method to distinguish lymphoplasmacytic lymphoma from other B cell neoplasms comprises obtaining a biological sample from a subject that presents symptoms of a B cell lymphoma, which symptom does not exclude a diagnosis of lymphoplasmacytic lymphoma.
  • Symptoms of a B cell lymphoma which do not exclude a diagnosis of LPL include asymptomatic localized or generalized peripheral lymphadenopathy, plasmacytic difference, bone marrow involvement, autoimmune thrombocytopenia, end organ damage (renal insufficiency), anemia, hyper-viscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, adenopathy, and an IgM serum paraprotein.
  • said determining comprises performing an assay to interrogate position 38182641 in chromosome 3p22.2.
  • the assay comprises allele specific polymerase chain reaction performed using an allele specific primer, wherein the allele specific primer hybridizes at or near its 3' end to the mutation at position 38182641 in chromosome 3p22.2.
  • the allele specific primer is SEQ ID NO: 5.
  • the method comprises obtaining a biological sample from a subject that presents symptoms of both LPL and at least one B cell neoplasm selected from the group consisting of nodal marginal zone lymphomas, extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma), splenic B cell marginal zone lymphoma, monoclonal gammopathy of undetermined significance and plasma cell myeloma, determining from the biological sample whether the subject has a mutation at position 38182641 in chromosome 3p22.2, and providing a report whether the subject has a mutation at position 38182641 in chromosome 3p22.2, wherein the presence of the mutation is indicative that the subject has lymphoplasmacytic lymphoma.
  • B cell neoplasm selected from the group consisting of nodal marginal zone lymphomas, extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma), splenic B
  • a method to treat lymphoplasmacytic lymphoma in a subject comprises selecting a subject on the basis that the subject has a mutation at position 38182641 in chromosome 3p22.2.
  • the subject also presents one or more symptoms or clinical features of LPL, such as, anemia, hyper-viscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, adenopathy, and an IgM serum paraprotein.
  • the subject is administered a myeloid differentiation primary response 88 (MYD88) inhibitor, an interleukin receptor associate kinase 1/4 (IRAK-1/4) inhibitor, and/or a Bruton's tyrosine kinase (BT ) inhibitor in an amount effective to treat lymphoplasmacytic lymphoma.
  • MYD88 inhibitor is a peptidomimetic compound ST2825.
  • the IRAK- 1/4 inhibitor is N-(2-Morpholinylethyl)-2-(3- nitrobenzoylamido)-benzimidazole.
  • the BTK inhibitor is Ibrutinib (PCI-32765).
  • a method for monitoring progression or recurrence of lymphoplasmacytic lymphoma in a subject comprises obtaining multiple biological samples of a subject over a period of time, determining from the multiple biological samples the level of a transcript comprising a mutation at position 38182641 in chromosome 3p22.2, wherein a change in the level of the transcript over the period of time is indicative of the progression or recurrence of LPL in the subject.
  • the subject is undergoing chemotherapy to treat LPL.
  • the level of the transcript is measured using quantitative real time polymerase chain reaction.
  • the quantitative real time polymerase chain reaction is performed using an allele specific primer, wherein the allele specific primer hybridizes at or near its 3' end to the mutation at position 38182641 in chromosome 3p22.2.
  • the allele specific primer is SEQ ID NO: 5.
  • a method for detecting a mutation at position 38182641 in chromosome 3p22.2 in a subject comprises obtaining a biological sample from the subject in need of such detection, determining from the biological sample whether the subject has a mutation at position 38182641 in chromosome 3p22.2 by allele specific polymerase chain reaction performed using an allele specific primer wherein the allele specific primer hybridizes at or near its 3' end to the mutation at position 38182641 in chromosome 3p22.2.
  • a method for facilitating the diagnosis of lymphoplasmacytic lymphoma in a subject comprises selecting a subject on the basis that the subject presents one or more of the following clinical features: anemia, hyper-viscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, adenopathy, and an IgM serum paraprotein, obtaining a biological sample of the subject, determining from the biological sample whether the subject has a mutation at position 38182641 in chromosome 3p22.2, and providing a report summarizing statistically significant results indicating that the subject has
  • lymphoplasmacytic lymphoma if the subject has the mutation.
  • the biological sample includes, but is not limited to, a sample of bone marrow, lymph node, spleen or blood.
  • the mutation results in a single nucleotide change from T to C in the myeloid differentiation primary response 88 (MYD88) gene.
  • the mutation results in an amino acid change from leucine to proline at position 265 in the myeloid differentiation primary response 88 protein.
  • the subject is a human.
  • the subject is suspected of LPL and presents one or more of the clinical features of LPL.
  • the presence of the mutation in a subject at position 38182641 in chromosome 3p22.2 is predictive of the risk of development of LPL.
  • the presence of the mutation at position 38182641 in chromosome 3p22.2 in a subject having an elevated (abnormal) level of monoclonal IgM serum paraprotein is predictive of the risk of development of LPL.
  • a method for predicting the risk of development of LPL is provided.
  • the method comprises selecting a subject on the basis that the subject has an elevated (abnormal) level of monoclonal IgM serum paraprotein, and determining whether the subject has a mutation at position 38182641 in chromosome 3p22.2, wherein the presence of the mutation is indicative that the subject is at an increased risk of developing LPL. It may even be that the few instances where the mutation was present in a subject who is diagnosed with a B cell neoplasm (other than LPL and subtype ABC of diffuse large B cell lymphoma) was a mistaken diagnosis.
  • FIG. 1 shows acquired uniparental disomy (aUPD) at chromosome 3p encompassing MYD88 as determined by WGS.
  • aUPD acquired uniparental disomy
  • FIG. 2 shows agarose gel-based AS-PCR assay for detection of MYD88 L265P.
  • the mutant MYD88 L265P allele can consistently be detected at a dilution of 0.1%.
  • Figure 3 shows the sensitivity and specificity of the real-time AS-PCR and scatter plot of comparison of MYD88 L265P positive and negative patients and healthy donors.
  • the MYD88 L265P mutant DNA (OCI-LY3) was diluted with the wild-type DNA (OCI- LY19) at the concentration as indicated in the amplification plot.
  • the mutant MYD88 5 L265P allele can be detected at a dilution of 0.08% (FIG. 3A).
  • FIG. 4 shows increased phosphorylation of BTK by western blotting with phospho-specific antibody in Waldenstrom's Macroglobulinemia (WM) cell lines, BCWM. l and MWCL-1 , compared to Multiple myeloma cell lines, ANBL6 and INA6. Antibody against total BTK was used as loading control. PCI-32765 significantly 0 blocked the BTK phosphorylation in WM cells.
  • WM Waldenstrom's Macroglobulinemia
  • FIG. 5 shows that PCI-32765 blocked the downstream NF-kB, MAPK, Stat3 signaling by significantly reducing the phosphorylation of ⁇ , ERK1/2 and Stat3 proteins in WM cell lines, BCWM. l and MWCL-1 , compared to multiple myeloma cell 25 lines, ANBL6 and INA6. Antibodies against corresponding total proteins and GAPDH were used as loading controls.
  • FIG. 6 shows that knockdown of MYD88 by lentiviral transduction, and/or use of a MYD88 inhibitor leads to decreased BTK phosphorylation.
  • FIG. 7 demonstrates that BTK inhibitor PCI-32765 induces apoptosis of MYD88 L265P expressing WM cells alone and in combination with MYD88 pathway inhibitor and IRAK 1/4 kinase inhibitor.
  • Apoptosis analysis was performed using Annexin V and PI staining after PCI-32765 treatment for 24hrs (FIG. 7A).
  • FIG. 7B apoptosis analysis was performed using annexin V and PI staining after PCI-32765 and MYD88 homodimerization inhibitor treatment for 24hrs.
  • PCI-32765 shows synergistic tumor cell killing in combination with an IRAK 1/4 kinase inhibitor (FIG. 7C).
  • the present invention in one aspect, relates to the surprising discovery of a somatic mutation in the myeloid differentiation primary response (MYD88) gene in patients with lymphoplasmacytic lymphoma.
  • the invention is based on the identification of a somatic mutation at position 38182641 in chromosome 3p22.2 which results in a single nucleotide change from T ⁇ C in the myeloid differentiation primary response (MYD88) gene, and a predicted non-synonymous change at amino acid position 265 from leucine to proline (L265P). While previous work has identified the same mutation in subtype ABC of diffuse large B cell lymphoma, this previous work did not make any association between the mutation and lymphoplasmacytic lymphoma.
  • the present invention provides diagnostic assays for facilitating or aiding in the diagnosis of lymphoplasmacytic lymphoma (LPL) in a subject.
  • LPL is a neoplasm of small B lymphocytes, plasma cytoid lymphocytes, and plasma cells, usually involving bone marrow (BM) and sometime lymph nodes and spleen.
  • Waldenstrom macroglobulinemia (WM) is found in a significant subset of patients with LPL and is defined as LPL with BM involvement and an IgM monoclonal gammopathy of any concentration.
  • a subject is selected for assessment of a mutation at position 38182641 in chromosome 3p22.2 on the basis that the subject is suspected of having LPL, and a biological sample of the subject is assessed for the presence of a mutation. The presence of the mutation is indicative that the subject has LPL.
  • selecting a subject means identifying a subject that presents one or more clinical features of LPL for further diagnostic analysis.
  • the one or more clinical features of LPL include anemia, hyper-viscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, adenopathy, and an IgM serum paraprotein.
  • a subject presenting two or more, three or more, four or more, five or more, six or more, or seven or more of these clinical features is selected.
  • the subject is selected by a medical practitioner (e.g., a doctor, nurse, clinical laboratory practitioner, genetic counselor, etc.), a healthcare organization, or a clinical laboratory.
  • Non-limiting examples of the biological sample include bone marrow, lymph node, spleen or blood.
  • Obtaining a biological sample of a subject means taking possession of a biological sample of the subject.
  • Obtaining a biological sample from a subject means removing a biological sample from the subject. Therefore, the person obtaining a biological sample of a subject and determining the presence of the mutation in the sample does not necessarily obtain the biological sample from the subject.
  • the biological sample may be removed from the subject by a medical practitioner (e.g., a doctor, nurse, or a clinical laboratory practitioner), and then provided to the person determining the presence of the mutation.
  • the biological sample may be provided to the person determining the mutation by the subject or by a medical practitioner (e.g., a doctor, nurse, or a clinical laboratory practitioner).
  • the person determining the mutation obtains a biological sample from the subject by removing the sample from the subject.
  • mutation means any change or difference in the nucleic acid or protein sequence of MYD88 as compared to the wild type sequence that results in the activation of MYD88 which leads to the activation of NF- ⁇ . Mutations include, but are not limited to, nonsense mutations, missense mutations, frameshift mutations, rearrangement mutations, insertion mutations and deletion mutations.
  • the mutation is a somatic mutation at position 38182641 in chromosome 3p22.2 which results in a single nucleotide change from T ⁇ C in the myeloid differentiation primary response (MYD88) gene, and a predicted non-synonymous change at amino acid position 265 from leucine to proline (L265P).
  • Detection methods include, but are not limited to, direct sequencing, DNAchip technologies, mass spectroscopy, polymerase chain reaction (PCR), allele specific polymerase chain reaction, real time polymerase chain reaction, reverse transcriptase PCR, electrophoretic mobility, nucleic acid hybridization, fluorescent in situ hybridization, and denaturing high performance liquid
  • mutations in the MYD88 gene may be detected by allele specific polymerase chain reaction (AS-PCR).
  • AS-PCR allele specific primers are used which hybridize at or near their 3' ends to a particular mutation in the MYD88 gene. If the mutation is not present, the 3 '-terminal mismatched primer does not initiate replication, and an amplification product is not observed.
  • only the forward primer or the reverse primer hybridizes at or near its 3' ends to a particular mutation in the MYD88 gene.
  • both the forward and the reverse primer hybridize at or near their 3' ends to a particular mutation in the MYD88 gene.
  • the allele specific primer is SEQ ID NO: 5.
  • the mutation is a somatic mutation at position 38182641 in chromosome 3p22.2 which results in a single nucleotide change from T— >C in the myeloid differentiation primary response (MYD88) gene, and a predicted non-synonymous change at amino acid position 265 from leucine to proline (L265P).
  • mutations in the MYD88 gene may be detected by the direct sequencing of nucleic acid molecules.
  • Techniques for the direct sequencing of DNA are well known in the art.
  • mutations may be detected by Sanger sequencing, which may include the use of a thermostable polymerase enzyme, a sequencing primer, dNTPs and limiting amounts of chain terminating fluorescently or radioactively labeled ddNTPs.
  • Polyacrylamide gel electrophoresis or another technique such as capillary electrophoresis may be used to separate the products of the sequencing reactions followed by the detection of the fluorescent or radioactive labels.
  • mutations in MYD88 could be determined using automated sequencing on an Applied Biosystems 3700 DNA Analyzer or 3730 1 DNA AnalyzerTM. Mutations may be identified by comparing the sequence of a subject to that of a wildtype individual or to reference sequences found in the public databases.
  • DNA chip technologies for the detection of mutations within the MYD88 gene.
  • DNA chip technologies allow for the identification of mutations within the sequences of the intention through the analysis of the hybridization patterns of a nucleic acid sample onto a high-density spatially addressable microarray of predetermined sequences.
  • one embodiment of the invention includes the use of a Transgenomic WaveTM machine for the dHPLC analysis of nucleic acids for the identification of heterozygous mutations or polymorphisms within the sequences of the invention.
  • the invention also contemplates the use of mass spectroscopy for the genotyping of mutations.
  • Mutant and wildtype nucleic acid molecules may differ in mass due to the different composition of wildtype and mutant sequences, allowing for the identification of mutations on the basis of the molecular mass of different nucleotide sequences.
  • the use of mass spectroscopy, and in particular Matrix Assisted Laser Desorption Ionisation Time of Flight (MALDI-TOF) mass spectroscopy for the genotyping of mutations is well known by those skilled in the relevant art.
  • MALDI-TOF Matrix Assisted Laser Desorption Ionisation Time of Flight
  • U.S. Pat. No. 6,043,031 describes a fast and highly accurate mass spectrometer based process for detecting a particular nucleic acid sequence.
  • the MassARRAYTM platform from SEQUENOMTM is an example of a commercially available system capable of genotyping single nucleotide polymorphisms and detecting the mutations in genes.
  • the present invention provides a method to distinguish lymphoplasmacytic lymphoma from other B cell neoplasms selected from the group consisting of nodal marginal zone lymphomas, extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma), splenic B cell marginal zone lymphoma, monoclonal gammopathy of undetermined significance and plasma cell myeloma.
  • the method comprises selecting or identifying a subject that presents one or more symptoms or clinical features of LPL which overlap with one or more symptoms of at least one of the B cell neoplasms described above.
  • the subject is an individual who is suspected of having either LPL or one of the other B cell neoplasm.
  • the subject is selected for further diagnostic analysis by a medical practitioner (e.g., a doctor, nurse, clinical laboratory practitioner, genetic counselor, etc.), a healthcare organization, or a clinical laboratory.
  • the one or more symptoms or clinical features of LPL include anemia, hyperviscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, adenopathy, and an IgM serum paraprotein.
  • the subject may also present one or more of the following clinical features or symptoms of other B cell neoplasms: asymptomatic localized or generalized peripheral lymphadenopathy, plasmacytic difference, bone marrow involvement, autoimmune thrombocytopenia, peripheral blood villous lymphocytes, end organ damage (hypercalcemia, renal insufficiency, bone lesions), recurrent infections, elevated creatine, hyperuricemia, and hypoalbunemia.
  • the subject suspected of having either LPL or one of the other B cell neoplasm is assessed for the presence of a mutation at position 38182641 in chromosome 3p22.2, wherein the presence of the mutation is indicative that the subject has LPL.
  • a report summarizing the results of the analysis i.e. the presence or absence of the mutation and any other information pertaining to the analysis could optionally be generated as part of the analysis (which may be interchangeably referred to herein as “providing” a report, “producing” a report, or “generating” a report).
  • Examples of reports may include, but are not limited to, reports in paper (such as computer-generated printouts of test results) or equivalent formats and reports stored on computer readable medium (such as a CD, computer hard drive, or computer network server, etc.).
  • Reports can be part of a database (such as a database of patient records, which may be a "secure database” that has security features that limit access to the report, such as to allow only the patient and the patient's medical practitioners to view the report, for example).
  • a database such as a database of patient records, which may be a "secure database” that has security features that limit access to the report, such as to allow only the patient and the patient's medical practitioners to view the report, for example.
  • reports can also be displayed on a computer screen (or the display of another electronic device or instrument).
  • a report can further be transmitted, communicated or reported (these terms may be used herein interchangeably), such as to the individual who was tested, a medical practitioner (e.g., a doctor, nurse, clinical laboratory practitioner, genetic counselor, etc.), a healthcare organization, a clinical laboratory, and/or any other party intended to view or possess the report.
  • a medical practitioner e.g., a doctor, nurse, clinical laboratory practitioner, genetic counselor, etc.
  • the act of 'transmitting' or 'communicating' a report can be by any means known in the art, based on the form of the report, and includes both oral and non-oral transmission.
  • "transmitting" or "communicating" a report can include delivering a report ("pushing") and/or retrieving ("pulling”) a report.
  • non-oral reports can be transmitted/communicated by such means as being physically transferred between parties (such as for reports in paper format), such as by being physically delivered from one party to another, or by being transmitted electronically or in signal form (e.g., via e-mail or over the internet, by facsimile, and/or by any wired or wireless communication methods known in the art), such as by being retrieved from a database stored on a computer network server, etc.
  • a method to treat LPL comprises selecting a subject on the basis that the subject has a mutation at position 38182641 in chromosome 3p22.2, and administering to the subject a myeloid differentiation primary response 88 (MYD88) inhibitor, an interleukin receptor associate kinase 1/4 (IRAK- 1/4) inhibitor, and/or a Bruton's tyrosine kinase (BTK) inhibitor in an amount effective to treat lymphoplasmacytic lymphoma.
  • MYD88 myeloid differentiation primary response 88
  • IRAK- 1/4 interleukin receptor associate kinase 1/4
  • BTK Bruton's tyrosine kinase
  • a non-limiting example of an MYD88 inhibitor includes the peptidomimetic compound ST2825 (WO 2006/06709).
  • a non-limiting example of an IRAK- 1/4 inhibitor is N-(2-Morpholinylethyl)-2-(3- nitrobenzoylamido)-benzimidazole.
  • BTK inhibitors useful in the instant invention block MYD88 L265P and BTK signaling.
  • a non-limiting example of a BTK inhibitor includes Ibrutinib (PCI-32765).
  • the method comprises selecting a subject on the basis that the subject has a mutation at position 38182641 in chromosome 3p22.2 and presents one or more symptoms of LPL.
  • the selected subject is treated using an effective amount of bortezomib (Velcade®), bendamestine, alemtuzumab, and/or rituximab, but not bisphosphonates or fludarabine.
  • the MYD88 inhibitor, IRAK- 1/4 inhibitor, and/or BTK inhibitor are administered in an effective amount.
  • An effective amount is a dose sufficient to provide a medically desirable result and can be determined by one of skill in the art using routine methods.
  • an effective amount is an amount which results in any improvement in the condition being treated.
  • an effective amount may depend on the type and extent of LPL being treated and/or use of one or more additional therapeutic agents. However, one of skill in the art can determine appropriate doses and ranges of therapeutic agents to use, for example based on in vitro and/or in vivo testing and/or other knowledge of compound dosages.
  • a maximum dose is used, that is, the highest safe dose according to sound medical judgment.
  • an effective amount is that amount which slows the progression of the disease, halts the progression of the disease, or reverses the progression of the disease.
  • An effective amount includes, but is not limited to, that amount necessary to slow, reduce, inhibit, ameliorate or reverse one or more symptoms associated with LPL.
  • such terms refer to a reduction in the levels of IgM serum paraprotein, anemia, hyper-viscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, and adenopathy.
  • An effective amount of a compound typically will vary from about 0.001 mg/kg to about 1000 mg/kg in one or more dose administrations, for one or several days
  • Actual dosage levels of the therapeutic agent can be varied to obtain an amount that is effective to achieve the desired therapeutic response for a particular patient, compositions, and mode of administration.
  • the selected dosage level depends upon the activity of the particular compound, the route of administration, the tissue being treated, and prior medical history of the patient being treated. However, it is within the skill of the art to start doses of the compound at levels lower than required to achieve the desired therapeutic effort and to gradually increase the dosage until the desired effect is achieved.
  • compositions can be administered orally, including sublingually, rectally, parenterally, intracisternally, intravaginally, intraperitoneal! y, topically and transdermally (as by powders, ointments, or drops), bucally, or nasally.
  • pharmaceutical preparations of the present invention may include or be diluted into a pharmaceutically-acceptable carrier.
  • pharmaceutically-acceptable carrier means one or more compatible fillers, diluants or other such substances, which are suitable for administration to a human or other mammal such as a dog, cat, or horse.
  • carrier denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application. The carriers are capable of being commingled with the preparations of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy or stability. Carriers suitable for oral, subcutaneous, intravenous, intramuscular, etc. formulations can be found in Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa.
  • a method for monitoring progression or recurrence of lymphoplasmacytic lymphoma in a subject comprises obtaining multiple biological samples of a subject over a period of time, determining from the multiple biological samples the level of a transcript comprising a mutation at position 38182641 in chromosome 3p22.2, wherein an increase in the level of the transcript over the period of time is indicative of the progression or recurrence of LPL in the subject.
  • a transcript comprising a mutation means MYD88 nucleic acid or protein that has a mutation at position 38182641 in chromosome 3p22.2.
  • the level of the transcript comprising a mutation at position 38182641 in chromosome 3p22.2 can be determined by any means known to one skilled in the art, including, but not limited to Western blot, Northern blot, and quantitative real time polymerase chain reaction.
  • quantitation of the transcript levels is accomplished by quantitative real-time PCR using the ABI PRISM® 7600, 7700, or 7900 Sequence Detection System (PE-Applied Biosystems, Foster City, Calif.) according to manufacturer's instructions. Methods of quantitative real-time PCR are well known in the art.
  • the quantitative real time polymerase chain reaction is performed using an allele specific primer, wherein the allele specific primer hybridizes at or near its 3' end to a mutation at position 38182641 in chromosome 3p22.2.
  • the allele specific primer is SEQ ID NO: 5.
  • the level of the transcript comprising the mutation is indicative of the state of the disease. In normal (healthy) subjects the mutation is absent. In diseased subjects, the transcript comprising the mutation is expressed at a level consistent with the status
  • a change in the level of the transcript comprising a mutation means that the amount or concentration of the transcript sufficiently changes over time.
  • a change in the level of the transcript over the period of time may be any statistically significant change which is detectable. Such a change may include, but is not limited to, about a 1 %, about a 10%, about a 20%, about a 40%, about a 80%, about a 2-fold, about a 4-fold, about an 8-fold, about a 20-fold, or about a 100-fold change over the time.
  • a "period of time" is intended to include a period of days, weeks, months or even years.
  • Multiple biological samples of the subject are obtained over a period of time, i.e. a biological sample is obtained periodically over time at various intervals.
  • a biological sample can be obtained at any interval.
  • a biological sample can be taken every day for weeks, months or years.
  • a biological sample can be obtained once a week, or six times a week for a period of weeks, months or years.
  • a biological sample is obtained once a week over a period of three months.
  • a biological sample is obtained once a month for a period of months, or years.
  • the subject is undergoing chemotherapy to treat LPL.
  • An increase in the level of the transcript over the period of time in a subject undergoing chemotherapy to treat LPL would indicate that there is progression of the disease and that the subject is not responding to the therapy.
  • a decrease in the level of the transcript over the period of time in a subject undergoing chemotherapy to treat LPL would indicate that the subject is responding to the therapy.
  • a method for detecting a mutation at position 38182641 in chromosome 3p22.2 in a subject comprises obtaining a biological sample from the subject in need of such detection, and determining from the biological sample whether the subject has a mutation at position 38182641 in chromosome 3p22.2 by allele specific polymerase chain reaction (AS- PCR).
  • AS-PCR allele specific polymerase chain reaction
  • the AS-PCR is performed using an allele specific primer wherein the allele specific primer hybridizes at or near its 3' end to the mutation at position 38182641 in chromosome 3p22.2.
  • the allele specific primer is SEQ ID NO: 5.
  • the mutation is a somatic mutation at position 38182641 in chromosome 3p22.2 which results in a single nucleotide change from T— >C in the myeloid differentiation primary response (MYD88) gene, and a predicted non- synonymous change at amino acid position 265 from leucine to proline (L265P).
  • a subject in need of detection may be a subject suspected of having LPL.
  • the subject may present one or more clinical features of LPL including, but not limited to anemia, hyper-viscosity, neuropathy, coagulopathies, splenomegaly, hepatomegaly, adenopathy, and an IgM serum paraprotein.
  • a subject in need of detection may be a subject suspected of having subtype ABC of diffuse large B cell lymphoma.
  • the subject may present one or more clinical features of subtype ABC of diffuse large B cell lymphoma including, but not limited to enlarged lymph node in the neck, groin or abdomen, fever, weight loss, and drenching night sweats.
  • a subject in need of detection may be a subject suspected of having gastric mucosa-associated lymphoid tissue (MALT) lymphoma.
  • MALT gastric mucosa-associated lymphoid tissue lymphoma.
  • the subject may present one or more clinical features of MALT including, but not limited to chronic inflammation
  • Helicobacter pyroli infection stomach pain, dyspepsia, nausea, constipation and anemia.
  • a likelihood ratio test for each variant (variant score) expressed in decibels (dB) was generated and reported.
  • High confidence somatic variants were identified using CGAT version 1.3 with a somatic score of 0.1 giving an estimated rate of one false somatic single nucleotide variant per 17.7 Mb of DNA.
  • Copy number was estimated by %GC normalized read depth, and acquired uniparental disomy (aUPD) was identified as copy-neutral loss of heterozygosity.
  • allele imbalance was determined by the percentage of reads mapping to the minor allele at heterozygous SNPs which was averaged over 500 Kb.
  • a set of PCR primers were designed to amplify a 726- bp fragment that covers the MYD88 L265P mutation (forward: 5'-ggg ata tgc tga act aag ttg cca c-3'(SEQ ID NO: 1) and reverse: 5'-gac gtg tct gtg aag ttg gca tct c-3' (SEQ ID NO: 2)). Twenty nanograms of genomic DNA were used for PCR amplification.
  • the amplified fragments were isolated by QIAquick gel extraction kit (Qiagen, CA) and sequenced using the forward primer 5 '-get gtt gtt aac cct ggg gtt gaa g-3' (SEQ ID NO: 3), and the reverse primer 5'-gac gtg tct gtg aag ttg gca tct c-3' (SEQ ED NO: 4).
  • CD 19+ and CD 138+ isolated BM cells from an unrelated cohort of 12 other WM patients; CD 19+ isolated BM cells from 8 IgM MGUS patients; CD 138+ isolated BM cells from 8 multiple myeloma (MM) patients; CD19+ isolated PB mononuclear cells from 12 healthy donors; as well as the BCWM. l, MWCL-1, and WM-WSU WM cell lines; the IgM secreting Ramos cell line, and the MM1.S, RPMI 8226, and U266 MM cell lines were also Sanger sequenced for MYD88. TA cloning and sequencing of at least 100 clones was also performed using the above primers for CD19+ isolated BM cells for 4 patients with IgM MGUS (Genewiz, S. Plainfield, NJ).
  • Tumor and normal genomes were both sequenced to an average of 66X (range 60-9 IX) coverage of mapped individual reads. The average gross mapped yield for these genomes was 186.89 (range 171.56-262.03 Gb).
  • a recurring sequence variant with a variant score of 189 (range 74-345) at position 38182641 in chromosome 3p22.2 which results in a single nucleotide change from T ⁇ C in the myeloid differentiation primary response (MYD88) gene, and a predicted non-synonymous change at amino acid position 265 from leucine to proline (L265P).
  • This variant was the most common of a median of 3,419 (range 2,540-4,01 1) somatic variants identified by WGS in the 10 paired patients using a somatic score of 0.1.
  • the MYD88 L265P variant was heterozygous, whereas in 4 patients an acquired UPD event (median 49.5 MB, range 48.5-50.0 MB) at 3p22.2 resulted in homozygous presence of the variant in at least a subset of tumor cells (Fig. 1A, B). These UPD events were absent in normal tissue for the 2 of 4 patients who had paired samples (Fig. 1C, D).
  • the MYD88 L265P variant was not found in the IgM secreting cell lines WM-WSU and Ramos, both of which carry t(8; 14), and in none of the myeloma cell lines. Furthermore, we did not detect the MYD88 L265P variant in CD 19+ selected B-cells from 12 healthy individuals, nor in tumor samples from 8 of 8 myeloma patients. By direct Sanger sequencing, the MYD88 L265 mutation was absent in 7 of 8 (87.5%) IgM MGUS patients whose characteristics are described in Table 2.
  • IgM MGUS might itself be heterogeneous, with acquisition of the MYD88 L265P leading to WM, while in other cases with wild type MYD88, a different oncogenic trajectory may result.
  • MYD88 has been discovered in significant yielding of a mutation in MYD88.
  • TLR Toll-like receptor
  • IL-1R interleukin- 1 receptor
  • All of the TLRs except for TLR3 use MYD88 to facilitate their signaling.
  • MYD88 is recruited to the activated receptor complex as a homodimer which then complexes with E AK4, leading to its
  • MYD88/IRAK4 complex then recruits and activates IRAKI and IRAK2.
  • Tumor necrosis factor receptor associated factor 6 (TRAF-6) is then activated by IRAKI leading to early NF- ⁇ activation, whereas IRAK2 facilitates late NF-KB activation.
  • TNF-6 Tumor necrosis factor receptor associated factor 6
  • the L265P mutation in MYD88 occurs at a residue that is highly conserved in evolution, and contributes to a ⁇ -sheet at the hydrophobic core of the domain.
  • MYD88 L265P mutation was absent in tumor samples from patients with the GCB subtype of DLBCL, and Burkitt's lymphoma.
  • the frequency of 90% observed for the MYD88 L265 variant in our studies from 2 independent cohorts of WM patients is far more extensive than that observed in DLBCL (29%) and MALT (6%) lymphomas.
  • NF- ⁇ signaling represents a critical determinant of WM cell growth and survival
  • targeting of tonic MYD88/IRAK signaling is of potential relevance to WM therapy.
  • the mutant-specific reverse primer was 5'- CCT TGT ACT TGA TGG GGA aCG-3' (SEQ ID NO: 5) and the wild-type-specific reverse primer was 5'-GCC TTG TAC TTG ATG GGG AaC A-3' (SEQ ID NO: 6).
  • the common forward primer was 5'-AAT GTG TGC CAG GGG TAC TTA G-3' (SEQ ID NO: 7).
  • PCR reaction was performed in a final volume of 25 ul with 50 nM of each primer and 50 ng DNA using PCR SuperMix High Fidelity (Life technology, CA). Thermal cycling conditions were: 2 min at 94°C, followed by 40 cycles of 94°C for 30s, 57°C for 30s, and 68°C for 30s, with a final extension at 68°C for 5 min.
  • the amplified PCR products (159-bp) were separated on 2% agarose gel. To confirm the sequence, PCR products were purified by QIA quick gel extraction kit (Qiagen, CA) and sequenced using both forward and reverse PCR primers.
  • Quantitative detection of the MYD88 L265P mutation was developed using the primers described above and Power S YBR® Green PCR Master Mix according to manufacturer's instruction on the ABI Prism 7500 Sequence Detection System (Applied Biosystems, Foster City, CA). Briefly, PCR reaction was performed in a final volume of 25 ⁇ with 25 nM of each primer and 50 ng DNA. Thermal cycling conditions were: 10 min at 950C, followed by 40 cycles of 95°C for 15s and 60°C for 60s. Each sample was assayed in triplicate. The standard curve for MYD88 L265P was generated by a serial dilution of the mutant DNA with the wild-type DNA (50%, 10%, 2%, 0.4%, 0.08%, and wild-type).
  • the forward primer is same as the one used for the AS-PCR (5'-AAT GTG TGC CAG GGG TAC TTA G-3' ; (SEQ ID NO: 7)) and the reverse primer is located at 53-bp downstream of the AS-PCR primer (5'-TGG TGT AGT CGC AGA CAG TGA-3' ; (SEQ ID NO: 8)).
  • Levels of the mutant MYD88 L265P in patient samples were calculated based on the value of delta CT and the standard curve.
  • the forward PCR primer 5' -GGG ATA TGC TGA ACT AAG TTG CCA C-3' (SEQ ID NO: 1) and reverse PCR primer 5'-GAC GTG TCT GTG AAG TTG GCA TCT C-3' (SEQ ED NO: 4) were designed to amplify a 726-bp fragment covering the MYD88 L265P site.
  • Amplified PCR products were isolated by QIA quick gel extraction kit (Qiagen, CA) and sequenced using the reverse PCR primer and a sequencing primer 5'-GCT GTT GTT AAC CCT GGG GTT GAA G-3' (SEQ ED NO: 3).
  • Sensitivity of the AS- PCR assay was assessed by a serial dilution of the DNA isolated from DLBCL cell line OCI-LY3 (homozygous MYD88 L265P) with the DNA from DLBCL cell line OCI- LY19 (wild-type MYD88 L265P).
  • the MYD88 L265P status of the cell lines was confirmed by Sanger sequencing (Fig. 2B).
  • the sensitivity assessments demonstrated that the mutant allele of MYD88 L265P can consistently be detected at a dilution of 0.1 % in the gel-based AS-PCR assay (Fig. 2C).
  • this real-time AS-PCR can detect the MYD88 L265P mutation at a dilution of 0.08% with more than 2 cycle differences from the wild-type DNA background. Correlation coefficient of the standard curve was 0.998 with a slope value of -3.5 (Fig. 3B). The melting curve analysis revealed that the MYD88 L265P mutant-specific amplicon melted at 840C (Fig. 3C). A minor non-specific amplification was only found in the dilution of 0.4% or lower with a melting peak at 80°C.
  • This cluster was determined as MYD88 L265P positive.
  • the gel-based AS-PCR and the real-time AS-PCR showed an exactly same result of determining the status of MYD88 L265P in this cohort.
  • the overall results suggest that a small subset of WM patients may not carry the MYD88 L265P mutation.
  • the entire coding region of the MYD88 gene was sequenced for the 10 patients who were negative for MYD88 L265P as determined by AS-PCR. No MYD88 mutation was found.
  • MYD88 L265P was initially reported in DLBCL as a gain-of-function mutation that promotes NF-kB and JAK-STAT3 signaling through activating the IRAK family of serine-threonine kinases. Interestingly, MYD88 L265P was frequently mutated in the ABC subtype of DLBCL (29%) but rare in the GCB subtype. We sought to evaluate the differences of clinical characteristics between the two clusters of WM patients determined by AS-PCR.
  • BM examination is essential in the clinical staging of non-Hodgkin's lymphomas (NHLs)
  • NDLs non-Hodgkin's lymphomas
  • Merli et al reported a comparison between histology and flow cytometry (FC) on the assessments of BM involvement in non-Hodgkin's lymphomas (NHLs) including LPL (Assessment of bone marrow involvement in non-Hodgkin's lymphomas:
  • Bruton's tyrosine kinase promotes B-cell receptor signaling along with B- cell expansion and survival through NF- ⁇ and MAPK.
  • MYD88 L265P is a widely expressed somatic mutation in tumor cells from WM patients.
  • MYD88 L265P promotes enhanced tumor cell survival through IRAK 1/4 mediated NF- ⁇ and MAPK signaling.
  • BTK was highly expressed and phosphorylated in MYD88-L265P expressing WM cells and PCI-32765 significantly blocked the BTK activation (FIG. 4). Increased phosphorylation of BTK was confirmed by western blotting with phospho-specific antibody in Waldenstrom's Macroglobulinemia (WM) cell lines, BCWM.l and MWCL- 1 , compared to Multiple myeloma cell lines, ANBL6 and ENA6. Antibody against total BTK was used as loading control. PCI-32765 significantly blocked the BTK
  • PCI32765 significantly reduced downstream NF-kB, MAPK and STAT3 signaling in WM cells (FIG. 5). In addition to significantly blocking the BTK activation, PCI-32765 also blocked the downstream NF-kB, MAPK, Stat3 signaling by significantly reduced the phosphorylation of ⁇ , ERK1/2 and Stat3 proteins in WM cell lines, BCWM. l and MWCL-1, compared to multiple myeloma cell lines, ANBL6 and INA6. Antibodies against corresponding total proteins and GAPDH were used as loading controls.
  • MYD88 knockdown leads to decreased BTK phosphorylation (FIG. 6).
  • MYD88 knockdown was confirmed by western blot in BCWM. l and MWCL- 1 cells. The knockdown of MYD88 reduced BTK phosphorylation compared with controls. MYD88 homodimerization inhibitory peptides significantly reduced BTK phosphorylation compared with control peptides. Antibodies against total BTK and/or GAPDH were used as loading control..
  • PCI-32765 Treatment with PCI-32765 induces apoptosis of MYD88 L265P expressing WM cells (FIG. 7A).
  • PCI-32765 shows robust tumor cell killing in combination with a MYD88 pathway inhibitor in primary WM patients bone marrow tumor cells (FIG. 7B).
  • PCI-32765 shows synergistic tumor cell killing in combination with an IRAK 1/4 kinase inhibitor (FIG. 7C).
  • BTK activation is facilitated by MYD88 pathway signaling in MYD88 L265P expressing WM cells, and participates in MYD88 downstream signaling.
  • Inhibition of BTK by PCI-32765 leads to robust tumor killing of MYD88 L265P expressing WM cells, which is potentiated by MYD88 pathway inhibitors.
  • lymphoplasmacytic cells were used in whole genome sequencing studies.

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Abstract

La présente invention concerne des tests de diagnostic permettant de faciliter le diagnostic d'un lymphome lymphoblasmocytaire (LPL). Le procédé comprend la détermination, dans un échantillon biologique du patient, de la présence d'une mutation en position 38182641 du chromosome 3p22.2, la présence de la mutation indiquant que le sujet est atteint d'un LPL. L'invention concerne également des thérapies ciblées, des procédés de suivi de l'évolution ou de la récurrence d'un LPL, et un essai en temps réel par amplification en chaîne par polymérase allèle spécifique, sensible et peu coûteux, permettant de déterminer de manière fiable et quantitative la mutation.
PCT/US2012/044956 2011-07-01 2012-06-29 Découverte d'une mutation somatique dans le gène myd88 du lymphome lymphoblasmocytaire WO2013006443A2 (fr)

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ES12807230.3T ES2624981T3 (es) 2011-07-01 2012-06-29 Descubrimiento de una mutación somática en el gen MYD88 en linfoma linfoplasmocitario
CA2840687A CA2840687C (fr) 2011-07-01 2012-06-29 Decouverte d'une mutation somatique dans le gene myd88 du lymphome lymphoblasmocytaire
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Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014166820A1 (fr) * 2013-04-08 2014-10-16 Bayer Pharma Aktiengesllschaft Utilisation de 2,3-dihydroimidazo[1,2-c]quinazolines substituées pour le traitement de lymphomes
WO2014190163A2 (fr) * 2013-05-22 2014-11-27 Children's Hospital Medical Center Polythérapie pour mds
WO2015038887A1 (fr) 2013-09-12 2015-03-19 Dana-Farber Cancer Institute Inc. Néthodes d'évaluation et de traitement de la macroglobulinémie de waldenström
WO2015085075A1 (fr) 2013-12-06 2015-06-11 Dana-Farber Cancer Institute, Inc. Procédés pour distinguer une macroglobulinémie de waldenström d'une gammopathie monoclonale igm de signification indéterminée
WO2017189999A1 (fr) 2016-04-29 2017-11-02 Dana-Farber Cancer Institute, Inc. Hck utilisé en tant que cible thérapeutique dans des maladies ayant des mutations de myd88
US10465247B2 (en) 2011-07-01 2019-11-05 Dana-Farber Cancer Institute, Inc. Discovery of a somatic mutation in MYD88 gene in lymphoplasmacytic lymphoma
WO2020040696A1 (fr) * 2018-08-21 2020-02-27 A. Menarini Biomarkers Singapore Pte Ltd Diagnostic cellulaire unique de lymphome vitréo-rétinien primaire
WO2021071922A1 (fr) 2019-10-08 2021-04-15 Dana-Farber Cancer Institute, Inc. Dérivé pyrazolopyrimidine comme inhibiteur hck pour l'utilisation en thérapie, en particulier de maladies à mutation myd88
US11254667B2 (en) 2016-08-17 2022-02-22 Children's Hospital Medical Center Substituted imidazo[1,2-A]pyridines as IRAK 1/4 and flt3 inhibitors
US11542261B2 (en) 2016-08-17 2023-01-03 Children's Hospital Medical Center Substituted Imidazo[1,2-a]-pyridines as IRAK 1/4 and FLT3 inhibitors
US11547696B2 (en) 2016-10-28 2023-01-10 Children's Hospital Medical Center Methods and compositions for treatment of myelodysplastic syndromes and/or acute myeloid leukemias

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3286334A4 (fr) 2015-04-20 2018-09-12 Neogenomics Laboratories, Inc. Procédé visant à augmenter la sensibilité d'un séquençage de dernière génération
UY36660A (es) * 2015-04-30 2016-11-30 Bayer Pharma AG Combinaciones de inhibidores de irak4
EP3195865A1 (fr) * 2016-01-25 2017-07-26 Bayer Pharma Aktiengesellschaft Combinaisons d'inhibiteurs d'irak4 et inhibiteurs de btk
US10227657B2 (en) 2015-07-01 2019-03-12 Neogenomics Laboratories, Inc. Method for high sensitivity detection of MYD88 mutations
US10253370B2 (en) 2015-08-17 2019-04-09 Neogenomics Laboratories, Inc. High-sensitivity sequencing to detect BTK inhibitor resistance
CN110229910A (zh) * 2019-07-08 2019-09-13 福建省肿瘤医院（福建省肿瘤研究所、福建省癌症防治中心） Myd88基因l265p突变检测试剂盒及检测方法
CN111593126A (zh) * 2020-06-22 2020-08-28 杭州千麦医学检验所有限公司 一种检测myd88基因l265p突变的引物和探针及高灵敏度检测方法
WO2023288306A2 (fr) * 2021-07-16 2023-01-19 University Of Pittsburgh - Of The Commonwealth System Of Higher Education Ciblage du gène myd88 in vitro et in vivo

Family Cites Families (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DK1212327T3 (da) 1999-09-17 2003-12-15 Abbott Gmbh & Co Kg Pyrazolopyrimidiner som terapeutiske midler
US6921763B2 (en) 1999-09-17 2005-07-26 Abbott Laboratories Pyrazolopyrimidines as therapeutic agents
ATE500837T1 (de) 2002-12-05 2011-03-15 Univ Arkansas Molekulare determinanten des multiplen myeloms und deren verwendung
BRPI0418031A (pt) 2003-12-22 2007-04-17 Gilead Sciences Inc inibidores de quinase fosfonato-substituìdos
WO2006067091A1 (fr) 2004-12-20 2006-06-29 Sigma-Tau Industrie Farmaceutiche Riunite S.P.A. Inhibiteurs d'homodimerisation de myd88
KR101315610B1 (ko) 2006-09-22 2013-10-10 파마시클릭스, 인코포레이티드 브루톤 티로신 키나제 억제제
HUE027165T2 (en) 2006-10-02 2016-08-29 Squibb & Sons Llc Human antibodies that bind to CXCR4 and their uses
US20120065201A1 (en) 2007-03-28 2012-03-15 Pharmacyclics, Inc. Inhibitors of bruton's tyrosine kinase
US8394816B2 (en) 2007-12-07 2013-03-12 Irene Ghobrial Methods of using [3.2.0] heterocyclic compounds and analogs thereof in treating Waldenstrom's Macroglobulinemia
US7824861B2 (en) * 2008-07-10 2010-11-02 National Tsing Hua University Method for quantitative analysis of transcripts with nucleotide polymorphism at specific site
BRPI0918211A2 (pt) 2008-12-23 2015-12-08 Genentech Inc métodos de identificação de um paciente, métodos de predição da responsividade de um paciente, métodos de monitoramento, métodos de otimização da eficácia terapêutica e kit para detecção do níveis de expressão de p1gf
MX2012009208A (es) 2010-02-08 2012-09-07 Msd Oss Bv Compuestos de 8-metil-1-fenil-imidazol[1, 5-a]pirazina.
US20120071497A1 (en) * 2010-06-03 2012-03-22 Pharmacyclics, Inc. Methods of treating abc-dlbcl using inhibitors of bruton's tyrosine kinase
WO2013006443A2 (fr) 2011-07-01 2013-01-10 Dana-Farber Cancer Institute, Inc. Découverte d'une mutation somatique dans le gène myd88 du lymphome lymphoblasmocytaire
JP6541350B2 (ja) 2011-11-09 2019-07-10 ブリストル−マイヤーズ スクイブ カンパニーＢｒｉｓｔｏｌ−Ｍｙｅｒｓ Ｓｑｕｉｂｂ Ｃｏｍｐａｎｙ 抗ｃｘｃｒ４抗体による血液悪性腫瘍の処置
US9604988B2 (en) 2012-07-27 2017-03-28 Riken Agent for treating or inhibiting recurrence of acute myeloid leukemia
WO2015038887A1 (fr) 2013-09-12 2015-03-19 Dana-Farber Cancer Institute Inc. Néthodes d'évaluation et de traitement de la macroglobulinémie de waldenström
WO2015085075A1 (fr) 2013-12-06 2015-06-11 Dana-Farber Cancer Institute, Inc. Procédés pour distinguer une macroglobulinémie de waldenström d'une gammopathie monoclonale igm de signification indéterminée
KR20230156443A (ko) 2016-03-28 2023-11-14 프레시지 바이오싸이언시스, 인크. 암 치료를 위한 제약학적 조합물
EP3448390A1 (fr) 2016-04-29 2019-03-06 Dana-Farber Cancer Institute, Inc. Hck utilisé en tant que cible thérapeutique dans des maladies ayant des mutations de myd88
CN107056786B (zh) 2016-10-14 2019-05-07 苏州明锐医药科技有限公司 阿卡替尼的制备方法

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See references of EP2726634A4 *

Cited By (29)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11739385B2 (en) 2011-07-01 2023-08-29 Dana-Farber Cancer Institute, Inc. Discovery of a somatic mutation in MYD88 gene in lymphoplasmacytic lymphoma
US10465247B2 (en) 2011-07-01 2019-11-05 Dana-Farber Cancer Institute, Inc. Discovery of a somatic mutation in MYD88 gene in lymphoplasmacytic lymphoma
KR20150138858A (ko) * 2013-04-08 2015-12-10 바이엘 파마 악티엔게젤샤프트 림프종 치료를 위한 치환된 2,3-디히드로이미다조[1,2-c]퀴나졸린의 용도
KR102304108B1 (ko) * 2013-04-08 2021-09-23 바이엘 파마 악티엔게젤샤프트 림프종 치료를 위한 치환된 2,3-디히드로이미다조[1,2-c]퀴나졸린의 용도
WO2014166820A1 (fr) * 2013-04-08 2014-10-16 Bayer Pharma Aktiengesllschaft Utilisation de 2,3-dihydroimidazo[1,2-c]quinazolines substituées pour le traitement de lymphomes
EA037577B1 (ru) * 2013-04-08 2021-04-16 Байер Фарма Акциенгезельшафт ПРИМЕНЕНИЕ 2-АМИНО-N-[7-МЕТОКСИ-8-(3-МОРФОЛИН-4-ИЛПРОПОКСИ)-2,3-ДИГИДРОИМИДАЗО[1,2-c]ХИНАЗОЛИН-5-ИЛ]ПИРИМИДИН-5-КАРБОКСАМИДА ИЛИ ЕГО ФИЗИОЛОГИЧЕСКИ ПРИЕМЛЕМОЙ СОЛИ ИЛИ ГИДРАТА И ФАРМАЦЕВТИЧЕСКОЙ КОМПОЗИЦИИ, СОДЕРЖАЩЕЙ УКАЗАННОЕ СОЕДИНЕНИЕ, ДЛЯ ЛЕЧЕНИЯ ИЛИ ПРОФИЛАКТИКИ НЕХОДЖКИНСКОЙ ЛИМФОМЫ (НХЛ)
EA031493B9 (ru) * 2013-04-08 2019-12-18 Байер Фарма Акциенгезельшафт Комбинация и фармацевтическая композиция для лечения или профилактики неходжкинской лимфомы (нхл)
US9999623B2 (en) 2013-04-08 2018-06-19 Bayer Pharma Aktiengesellschaft Use of substituted 2,3-dihydroimidazo[1,2-c]quinazolines for treating lymphomas
EA031493B1 (ru) * 2013-04-08 2019-01-31 Байер Фарма Акциенгезельшафт Комбинация и фармацевтическая композиция для лечения или профилактики неходжкинской лимфомы (нхл)
US10226469B2 (en) 2013-04-08 2019-03-12 Bayer Pharma Aktiengesellschaft Use of substituted 2,3-dihydroimidazo[1,2-C]quinazolines for treating lymphomas
WO2014190163A3 (fr) * 2013-05-22 2015-01-29 Children's Hospital Medical Center Polythérapie pour mds
US9168257B2 (en) 2013-05-22 2015-10-27 Children's Hospital Medical Center Combination therapy for MDS
WO2014190163A2 (fr) * 2013-05-22 2014-11-27 Children's Hospital Medical Center Polythérapie pour mds
US9504706B2 (en) 2013-05-22 2016-11-29 Children's Hospital Medical Center Combination therapy for MDS
US9855273B2 (en) 2013-05-22 2018-01-02 Children's Hospital Medical Center Combination therapy for MDS
EP3044338A1 (fr) * 2013-09-12 2016-07-20 Dana-Farber Cancer Institute, Inc. Néthodes d'évaluation et de traitement de la macroglobulinémie de waldenström
US10526660B2 (en) 2013-09-12 2020-01-07 Dana-Farber Cancer Institute, Inc. Methods for evaluating and treating Waldenstrom's macroglobulinemia
WO2015038887A1 (fr) 2013-09-12 2015-03-19 Dana-Farber Cancer Institute Inc. Néthodes d'évaluation et de traitement de la macroglobulinémie de waldenström
EP3044338A4 (fr) * 2013-09-12 2017-04-26 Dana-Farber Cancer Institute, Inc. Néthodes d'évaluation et de traitement de la macroglobulinémie de waldenström
US10612095B2 (en) 2013-12-06 2020-04-07 Dana-Farber Cancer Institute, Inc. Methods to distinguish Waldenström's Macroglobulinemia from IgM monoclonal gammopathy of undetermined significance
AU2014360426B2 (en) * 2013-12-06 2020-05-07 Dana-Farber Cancer Institute, Inc. Methods to distinguish Waldenstrom's Macroglobulinemia from IgM monoclonal gammopathy of undetermined significance
WO2015085075A1 (fr) 2013-12-06 2015-06-11 Dana-Farber Cancer Institute, Inc. Procédés pour distinguer une macroglobulinémie de waldenström d'une gammopathie monoclonale igm de signification indéterminée
US10525060B2 (en) 2016-04-29 2020-01-07 Dana-Farber Cancer Institute, Inc. HCK as a therapeutic target in MYD88 mutated diseases
WO2017189999A1 (fr) 2016-04-29 2017-11-02 Dana-Farber Cancer Institute, Inc. Hck utilisé en tant que cible thérapeutique dans des maladies ayant des mutations de myd88
US11254667B2 (en) 2016-08-17 2022-02-22 Children's Hospital Medical Center Substituted imidazo[1,2-A]pyridines as IRAK 1/4 and flt3 inhibitors
US11542261B2 (en) 2016-08-17 2023-01-03 Children's Hospital Medical Center Substituted Imidazo[1,2-a]-pyridines as IRAK 1/4 and FLT3 inhibitors
US11547696B2 (en) 2016-10-28 2023-01-10 Children's Hospital Medical Center Methods and compositions for treatment of myelodysplastic syndromes and/or acute myeloid leukemias
WO2020040696A1 (fr) * 2018-08-21 2020-02-27 A. Menarini Biomarkers Singapore Pte Ltd Diagnostic cellulaire unique de lymphome vitréo-rétinien primaire
WO2021071922A1 (fr) 2019-10-08 2021-04-15 Dana-Farber Cancer Institute, Inc. Dérivé pyrazolopyrimidine comme inhibiteur hck pour l'utilisation en thérapie, en particulier de maladies à mutation myd88

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ES2624981T3 (es) 2017-07-18
US11739385B2 (en) 2023-08-29
US20140249142A1 (en) 2014-09-04
CA2840687A1 (fr) 2013-01-10
EP2726634A4 (fr) 2015-03-04
WO2013006443A3 (fr) 2013-03-14
EP2726634A2 (fr) 2014-05-07
CA2840687C (fr) 2020-04-28
US10465247B2 (en) 2019-11-05
US20200149114A1 (en) 2020-05-14
EP2726634B1 (fr) 2017-02-22

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